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Title: Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering

Abstract

Single-particle experiments using X-ray Free Electron Lasers produce more than 105 snapshots per hour, consisting of an admixture of blank shots (no particle intercepted), and exposures of one or more particles. Experimental data sets also often contain unintentional contamination with different species. We present an unsupervised method able to sort experimental snapshots without recourse to templates, specific noise models, or user-directed learning. The results show 90% agreement with manual classification.

Authors:
 [1];  [1];  [2];  [3];  [4];  [5];  [5];  [5];  [6];  [7];  [8];  [8];  [9];  [2];  [10];  [6];  [3];  [11];  [11];  [6] more »;  [12];  [5];  [6];  [3];  [7];  [13];  [14];  [13];  [15];  [5];  [13];  [12];  [15];  [16];  [6];  [7];  [12];  [17];  [6];  [9];  [16];  [13];  [12];  [11];  [11];  [12];  [6];  [3];  [2];  [12];  [7];  [13];  [7];  [12]; ;  [15];  [3];  [11];  [15];  [6];  [5];  [1] « less
+ Show Author Affiliations
  1. Univ. of Wisconsin, Milwaukee, WI (United States)
  2. Aix-Marseille Univ., Marseille (France)
  3. Swedish Univ. of Agricultural Sciences, Uppsala (Sweden)
  4. Uppsala Univ. (Sweden)
  5. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)
  6. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Center for Free-Electron Laser Science
  7. SLAC National Accelerator Lab., Menlo Park, CA (United States). Photon Ultrafast Laser Science and Engineering Inst. (PULSE)
  8. SLAC National Accelerator Lab., Menlo Park, CA (United States). Linac Coherent Light Source (LCLS)
  9. Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany). Center for Free-Electron Laser Science; Univ. of Hamburg (Germany)
  10. European X-ray Free-Electron Laser (XFEL), Hamburg (Germany)
  11. Max Planck Advanced Study Group, Hamburg (Germany); Max Planck Inst. fuer Kernphysik, Heidelberg (Germany)
  12. Max Planck Advanced Study Group, Hamburg (Germany); Max Planck Inst. fuer Medizinische Forschung, Jahnstrasse (Germany)
  13. PNSensor GmbH, Munich (Germany)
  14. Max Planck Inst. fuer Medizinische Forschung, Jahnstrasse (Germany)
  15. Max Planck Inst. fuer Extraterrestrische Physik, Garching (Germany); Max Planck Inst. Halbleiterlabor, Munchen (Germany)
  16. Elettra Sincrotrone Trieste (Italy)
  17. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Publication Date:
Research Org.:
Univ. of Wisconsin, Milwaukee, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1598219
Grant/Contract Number:  
SC0002164
Resource Type:
Accepted Manuscript
Journal Name:
Optics Express
Additional Journal Information:
Journal Volume: 19; Journal Issue: 17; Journal ID: ISSN 1094-4087
Publisher:
Optical Society of America (OSA)
Country of Publication:
United States
Language:
English
Subject:
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Citation Formats

Yoon, Chun Hong, Schwander, Peter, Abergel, Chantal, Andersson, Inger, Andreasson, Jakob, Aquila, Andrew, Bajt, Saša, Barthelmess, Miriam, Barty, Anton, Bogan, Michael J., Bostedt, Christoph, Bozek, John, Chapman, Henry N., Claverie, Jean-Michel, Coppola, Nicola, DePonte, Daniel P., Ekeberg, Tomas, Epp, Sascha W., Erk, Benjamin, Fleckenstein, Holger, Foucar, Lutz, Graafsma, Heinz, Gumprecht, Lars, Hajdu, Janos, Hampton, Christina Y., Hartmann, Andreas, Hartmann, Elisabeth, Hartmann, Robert, Hauser, Gunter, Hirsemann, Helmut, Holl, Peter, Kassemeyer, Stephan, Kimmel, Nils, Kiskinova, Maya, Liang, Mengning, Loh, Ne-Te Duane, Lomb, Lukas, Maia, Filipe R. N. C., Martin, Andrew V., Nass, Karol, Pedersoli, Emanuele, Reich, Christian, Rolles, Daniel, Rudek, Benedikt, Rudenko, Artem, Schlichting, Ilme, Schulz, Joachim, Seibert, Marvin, Seltzer, Virginie, Shoeman, Robert L., Sierra, Raymond G., Soltau, Heike, Starodub, Dmitri, Steinbrener, Jan, Stier, Gunter, Strüder, Lothar, Svenda, Martin, Ullrich, Joachim, Weidenspointner, Georg, White, Thomas A., Wunderer, Cornelia, and Ourmazd, Abbas. Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering. United States: N. p., 2011. Web. doi:10.1364/OE.19.016542.
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Yoon, Chun Hong, Schwander, Peter, Abergel, Chantal, Andersson, Inger, Andreasson, Jakob, Aquila, Andrew, Bajt, Saša, Barthelmess, Miriam, Barty, Anton, Bogan, Michael J., Bostedt, Christoph, Bozek, John, Chapman, Henry N., Claverie, Jean-Michel, Coppola, Nicola, DePonte, Daniel P., Ekeberg, Tomas, Epp, Sascha W., Erk, Benjamin, Fleckenstein, Holger, Foucar, Lutz, Graafsma, Heinz, Gumprecht, Lars, Hajdu, Janos, Hampton, Christina Y., Hartmann, Andreas, Hartmann, Elisabeth, Hartmann, Robert, Hauser, Gunter, Hirsemann, Helmut, Holl, Peter, Kassemeyer, Stephan, Kimmel, Nils, Kiskinova, Maya, Liang, Mengning, Loh, Ne-Te Duane, Lomb, Lukas, Maia, Filipe R. N. C., Martin, Andrew V., Nass, Karol, Pedersoli, Emanuele, Reich, Christian, Rolles, Daniel, Rudek, Benedikt, Rudenko, Artem, Schlichting, Ilme, Schulz, Joachim, Seibert, Marvin, Seltzer, Virginie, Shoeman, Robert L., Sierra, Raymond G., Soltau, Heike, Starodub, Dmitri, Steinbrener, Jan, Stier, Gunter, Strüder, Lothar, Svenda, Martin, Ullrich, Joachim, Weidenspointner, Georg, White, Thomas A., Wunderer, Cornelia, & Ourmazd, Abbas. Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering. United States. https://doi.org/10.1364/OE.19.016542
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Yoon, Chun Hong, Schwander, Peter, Abergel, Chantal, Andersson, Inger, Andreasson, Jakob, Aquila, Andrew, Bajt, Saša, Barthelmess, Miriam, Barty, Anton, Bogan, Michael J., Bostedt, Christoph, Bozek, John, Chapman, Henry N., Claverie, Jean-Michel, Coppola, Nicola, DePonte, Daniel P., Ekeberg, Tomas, Epp, Sascha W., Erk, Benjamin, Fleckenstein, Holger, Foucar, Lutz, Graafsma, Heinz, Gumprecht, Lars, Hajdu, Janos, Hampton, Christina Y., Hartmann, Andreas, Hartmann, Elisabeth, Hartmann, Robert, Hauser, Gunter, Hirsemann, Helmut, Holl, Peter, Kassemeyer, Stephan, Kimmel, Nils, Kiskinova, Maya, Liang, Mengning, Loh, Ne-Te Duane, Lomb, Lukas, Maia, Filipe R. N. C., Martin, Andrew V., Nass, Karol, Pedersoli, Emanuele, Reich, Christian, Rolles, Daniel, Rudek, Benedikt, Rudenko, Artem, Schlichting, Ilme, Schulz, Joachim, Seibert, Marvin, Seltzer, Virginie, Shoeman, Robert L., Sierra, Raymond G., Soltau, Heike, Starodub, Dmitri, Steinbrener, Jan, Stier, Gunter, Strüder, Lothar, Svenda, Martin, Ullrich, Joachim, Weidenspointner, Georg, White, Thomas A., Wunderer, Cornelia, and Ourmazd, Abbas. Fri . "Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering". United States. https://doi.org/10.1364/OE.19.016542. https://www.osti.gov/servlets/purl/1598219.
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@article{osti_1598219,
title = {Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering},
author = {Yoon, Chun Hong and Schwander, Peter and Abergel, Chantal and Andersson, Inger and Andreasson, Jakob and Aquila, Andrew and Bajt, Saša and Barthelmess, Miriam and Barty, Anton and Bogan, Michael J. and Bostedt, Christoph and Bozek, John and Chapman, Henry N. and Claverie, Jean-Michel and Coppola, Nicola and DePonte, Daniel P. and Ekeberg, Tomas and Epp, Sascha W. and Erk, Benjamin and Fleckenstein, Holger and Foucar, Lutz and Graafsma, Heinz and Gumprecht, Lars and Hajdu, Janos and Hampton, Christina Y. and Hartmann, Andreas and Hartmann, Elisabeth and Hartmann, Robert and Hauser, Gunter and Hirsemann, Helmut and Holl, Peter and Kassemeyer, Stephan and Kimmel, Nils and Kiskinova, Maya and Liang, Mengning and Loh, Ne-Te Duane and Lomb, Lukas and Maia, Filipe R. N. C. and Martin, Andrew V. and Nass, Karol and Pedersoli, Emanuele and Reich, Christian and Rolles, Daniel and Rudek, Benedikt and Rudenko, Artem and Schlichting, Ilme and Schulz, Joachim and Seibert, Marvin and Seltzer, Virginie and Shoeman, Robert L. and Sierra, Raymond G. and Soltau, Heike and Starodub, Dmitri and Steinbrener, Jan and Stier, Gunter and Strüder, Lothar and Svenda, Martin and Ullrich, Joachim and Weidenspointner, Georg and White, Thomas A. and Wunderer, Cornelia and Ourmazd, Abbas},
abstractNote = {Single-particle experiments using X-ray Free Electron Lasers produce more than 105 snapshots per hour, consisting of an admixture of blank shots (no particle intercepted), and exposures of one or more particles. Experimental data sets also often contain unintentional contamination with different species. We present an unsupervised method able to sort experimental snapshots without recourse to templates, specific noise models, or user-directed learning. The results show 90% agreement with manual classification.},
doi = {10.1364/OE.19.016542},
journal = {Optics Express},
number = 17,
volume = 19,
place = {United States},
year = {Fri Aug 12 00:00:00 EDT 2011},
month = {Fri Aug 12 00:00:00 EDT 2011}
}
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https://doi.org/10.1364/OE.19.016542
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